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+ FROM continuumio/miniconda3
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+ MAINTAINER Nick Waters <
[email protected] >
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+ RUN conda install -c anaconda matplotlib docopt tqdm wget pyyaml git
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+ RUN conda install -c bioconda pysam --update-deps
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+ RUN git clone https://github.com/DRL/blobtools.git
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+ WORKDIR blobtools
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+
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+ RUN ./blobtools -h
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+ # RUN ./blobtools create -i example/assembly.fna -b example/mapping_1.bam -t example/blast.out -o example/test
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+ RUN wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz -P data/
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+ RUN tar zxf data/taxdump.tar.gz -C data/ nodes.dmp names.dmp
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+ RUN ./blobtools nodesdb --nodes data/nodes.dmp --names data/names.dmp
Original file line number Diff line number Diff line change @@ -57,6 +57,18 @@ Create blobplot
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```
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Usage
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-----
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- ```
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- ./blobtools --help
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- ```
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+ ```
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+ ./blobtools --help
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+ ```
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+
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+ Docker
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+ ------
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+
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+ A docker container can be build using the following command:
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+ ```
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+ docker build -t drl/blobtools .
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+ ```
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+ This docker image can be run with sample data as follows:
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+ ```
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+ docker run -v $PWD/example:/example/ -t drl/blobtools ./blobtools create -i /example/assembly.fna -b /example/mapping_1.sorted.bam -t /example/blast.out -o /example/test
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+ ```
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